Help:Known problems

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===WikiPathways Editor Usage===
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The WikiPathways Editor is the PathVisio program.
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On this page you'll find some known problems with WikiPathways.  
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* If you have never edited or built a pathway model before, we would advise you to use our online learning tool [http://academy.wikipathways.org/ WikiPathways Academy] first.
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'''If your problem is not on this list''', please check our '''[http://developers.pathvisio.org/report bug tracker]''' or send an email to our '''[http://groups.google.com/group/wikipathways-discuss Google group]'''.
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* If you directly want to start editing, please download the [https://www.pathvisio.org/downloads/ local PathVisio installation] from the PathVisio website, and install the [https://www.pathvisio.org/plugin/wikipathways-plugin/ WikiPathways plugin] from within PathVisio.
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Please be aware that new users (starting in 2019) need to request access to use the WikiPathways plugin; which can be done [http://plugins.pathvisio.org/wp-client/request-webservice-access/ here] or through sending a message to our team on our [https://groups.google.com/forum/#!forum/wikipathways-discuss google discussion forum].
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===Java Warnings and Blocks===
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* Save your pathway by clicking '''Plugins > WikiPathways > Update'''. You will be asked to describe your edits.  
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There is a battle going on between Java, operating systems and browsers, and we are caught in the middle. While we work on the long-term solution of replacing our Java Applet editor with a JavaScript editor, we have recommendations and fixes for your particular OS and Java combination. [http://groups.google.com/group/wikipathways-discuss Let us know] if you have another setup or if these don't work for you.
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* That's it!
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'''''If you update your OS or Java version (often this is done automatically with minimal confirmation from you), then you'll need to revisit this table and perform the recommended setup steps.'''''
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===Java Security Settings===
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To enable direct-launch of the WikiPathways editor on MacOS, it is necessary to add the Java Security exceptions for WikiPathways. To do this, go to '''System Preferences > Java > Security'''. In the '''Exceptions Site List''', add both https://www.wikipathways.org and https://wikipathways.org. [https://www.youtube.com/watch?v=uUH1JVgnkug This video] shows how to add security exceptions. More details on MacOS Java Security are available [https://www.java.com/en/download/help/jcp_security.xml here].
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# Check your operating system version
 
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#* Mac: Apple menu > About this Mac
 
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#* Win: Start > Computer > Properties
 
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# Check your Java version (Note: versions 1.7.x = "Java 7" and versions 1.8.x = "Java 8")
 
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#* Mac: Open Terminal.app and type: java -version
 
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#* Win: Open Command and type: java -version
 
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# Find recommendations and fixes for your setup in the table below
 
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{| class="wikitable"
 
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!Operating System!!Java Version!!Browser!!Recommendations and fixes
 
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|MacOS 10.9
 
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|Java 7 & 8
 
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| Chrome or Firefox
 
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| Enable Java Applets and set Java security exceptions [https://www.youtube.com/watch?v=uUH1JVgnkug (see video)]
 
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|-
 
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|MacOS 10.10
 
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|Java 7
 
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|
 
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| coming soon...
 
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|-
 
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|MacOS 10.10
 
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|Java 8
 
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|
 
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| coming soon...
 
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|-
 
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|colspan="4"|
 
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|-
 
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|Win 7 (32 bit)
 
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|Java 8 (32 bit)
 
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|
 
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| coming soon...
 
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|-
 
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|Win 7 (64 bit)
 
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|Java 7 (32 bit)
 
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|
 
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| coming soon...
 
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|-
 
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|Win 7 (64 bit)
 
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|Java 8 (32 bit)
 
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|
 
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| coming soon...
 
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|-
 
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|Win 7 (64 bit)
 
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|Java 7 (64 bit)
 
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|
 
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| coming soon...
 
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|-
 
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|Win 7 (64 bit)
 
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|Java 8 (64 bit)
 
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|
 
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| coming soon...
 
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|-
 
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|Win 8.1 (64 bit)
 
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|Java 7 (64 bit)
 
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|
 
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| coming soon...
 
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|-
 
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|Win 8.1 (64 bit)
 
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|Java 8 (64 bit)
 
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|
 
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| coming soon...
 
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|}
 
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{{TutorialVideo|JyaLTAAn9SQ|200|Warnings you can ignore}}
 
===Ignorable Java Warnings===
===Ignorable Java Warnings===
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Even when your setup is configured properly, you may still see Java Security Warnings.  They look scary, but they are harmless.  If the warning says, "Location: http://wikipathways.org" then you can click through it and get to our Java Applet editor. Here's a super short video showing the errors to expect.
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Even when your setup is configured properly, you may still see Java Security Warnings.  They look scary, but they are harmless. These are simply due to the fact that we refuse to pay Apple to authorize our free and open source software. We are pursuing a free alternative through a non-profit collaborationBut, ultimately, if the warning says, "Location: <nowiki>http://wikipathways.org</nowiki>" then you can click through it and get to our Java Applet editor. Here's a [https://www.youtube.com/watch?v=JyaLTAAn9SQ super short video] showing errors you can expect and safely ignore.
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=== No Java installed ===
=== No Java installed ===
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For details see [http://www.pathvisio.org/documentation/faqs/#SecurityError the Pathvisio FAQ]
For details see [http://www.pathvisio.org/documentation/faqs/#SecurityError the Pathvisio FAQ]
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=== Other Problems ===
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'''If your problem is not on this list''', please check our '''[https://github.com/pathvisio/pathvisio/issues bug tracker]''' or send an email to our  '''[http://groups.google.com/group/wikipathways-discuss Google group]'''.
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Current revision

Contents

WikiPathways Editor Usage

The WikiPathways Editor is the PathVisio program.

  • If you have never edited or built a pathway model before, we would advise you to use our online learning tool WikiPathways Academy first.

Please be aware that new users (starting in 2019) need to request access to use the WikiPathways plugin; which can be done here or through sending a message to our team on our google discussion forum.

  • Save your pathway by clicking Plugins > WikiPathways > Update. You will be asked to describe your edits.
  • That's it!

Java Security Settings

To enable direct-launch of the WikiPathways editor on MacOS, it is necessary to add the Java Security exceptions for WikiPathways. To do this, go to System Preferences > Java > Security. In the Exceptions Site List, add both https://www.wikipathways.org and https://wikipathways.org. This video shows how to add security exceptions. More details on MacOS Java Security are available here.

Ignorable Java Warnings

Even when your setup is configured properly, you may still see Java Security Warnings. They look scary, but they are harmless. These are simply due to the fact that we refuse to pay Apple to authorize our free and open source software. We are pursuing a free alternative through a non-profit collaboration. But, ultimately, if the warning says, "Location: http://wikipathways.org" then you can click through it and get to our Java Applet editor. Here's a super short video showing errors you can expect and safely ignore.

No Java installed

You need to have Java installed to be able to edit pathways. If you only see a grey box when you click the edit button below the pathway image, please check if you have Java installed (version JSE 5 or above). You can test if Java is working in your browser here and download Java here.

Javascript disabled

You need to have javascript enabled in your browser. Click here to see how to enable javascript for your browser.

Strange error while starting Java

Sometimes a dialog with "NullPointerException" or "InvocationTargetException" appears when you try to start the edit applet. In this case it may help to clear the Java Applet Cache. In Windows XP, you do this as follows:

  1. Go to Start -> Control Panel
  2. (In Classic View) click on the icon Labeled Java
  3. In the Java Control Panel dialog, in the general tab, under the heading Temporary Internet Files click on Settings
  4. Click Delete Files. This will only delete temporary files that are safe to delete.
  5. Close the browser completely, then try WikiPathways again.

On a Mac:

  1. Open /Applications/Utilities/Java Preferences
  2. Click on Network tab
  3. Click on Delete Files and click OK
  4. Close the browser completely, then try WikiPathways again

Editor does not load and you just see a black window

In this case it might help to clear the Java Applet Cache. In Windows XP, you do this as follows:

  1. Go to Start -> Control Panel
  2. (In Classic View) click on the icon Labeled Java
  3. In the Java Control Panel dialog, in the general tab, under the heading Temporary Internet Files click on Settings
  4. Click Delete Files. This will only delete temporary files that are safe to delete.
  5. Close the browser completely, then try WikiPathways again.

Wrong Java version on Ubuntu

Older Ubuntu linux distribution came with the gij (GNU libgcj) Java virtual machine, while newer versions come with the icedtea plugins. In order to make WikiPathways work correctly, you will need to replace this with Oracle's JVM. Details on how to install this can be found here.

Application blocked by Security Setting

In the latest Java update the security settings for self-signed applications have been adapted (Java 7 Update 51). Self-Signed applications, like Pathvisio, are blocked on high security level. For details see the Pathvisio FAQ

Other Problems

If your problem is not on this list, please check our bug tracker or send an email to our Google group.

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